Imputation fails with error: reheader: invalid option -- 'O'

[Nicklas Nordborg]

java.lang.RuntimeException: reheader: invalid option -- 'O'

About:   Modify header of VCF/BCF files, change sample names.
Usage:   bcftools reheader [OPTIONS] <in.vcf.gz>

Options:
    -f, --fai FILE             update sequences and their lengths from the .fai file
    -h, --header FILE          new header
    -o, --output FILE          write output to a file [standard output]
    -s, --samples FILE         new sample names
    -T, --temp-prefix PATH     template for temporary file name [/tmp/bcftools.XXXXXX]
        --threads INT          use multithreading with <int> worker threads (BCF only) [0]

Example:
   # Write out the header to be modified
   bcftools view -h old.bcf > header.txt

   # Edit the header using your favorite text editor
   vi header.txt

   # Reheader the file
   bcftools reheader -h header.txt -o new.bcf old.bcf

Failed to read from standard input: unknown file type
srun: error: cnl01: task 0: Exited with exit code 255
  at net.sf.basedb.opengrid.service.OpenGridService.updateJobStatusInBase(OpenGridService.java:888)
  at net.sf.basedb.opengrid.service.OpenGridService.processAsyncRequests(OpenGridService.java:576)
  at net.sf.basedb.opengrid.service.OpenGridService$JobStatusTimerTask.run(OpenGridService.java:933)
  at net.sf.basedb.util.timer.ThreadTimerTask$1.run(ThreadTimerTask.java:94)
  at java.base/java.lang.Thread.run(Thread.java:833)

The -O (=output format) is typically available on all bcftools command but for some reason not for the 'reheader' command.

[Nicklas Nordborg]

Milestone renamed

[Nicklas Nordborg]

In 7799:

Fixes #1608: Imputation fails with error: reheader: invalid option -- 'O'

Removed the -Ou option.